Single cell UOW (excluding Slide TS36)

Intensities of Differentially Expressed Markers for Stem cells condition

Project description: Initial datasets shared by Australian collaborators (Tassiani Sarretto, Helena Anastacio). Three conditions (stem cells, cells grown for 7 and 14 days). 12 replicates per condition. One slide (TS36) including cells grown 7 days was excluded from this analysis (possible batch effects...?)

Date: 2023-05-30

Config: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/plots_without_TS36/config_QC_stem.yml

Notebook version: v0.2.0.post3+g966cb55.d20230408 (git-commit: 9f02807)

Report parameters

• Biological key: growthConditions
• Slide key: slide
• Process slides independently: False
• Replicate key: replicate_nb_overall
• Masking key: None
• AnnData pattern: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/anndatas/{slide}-well{well}-{row}{col}.h5ad
• AnnData type: AnnDatas downloaded from Metaspace
• Metadata file path: /Users/alberto-mac/Documents/DA_ESPORTARE/LOCAL_EMBL_FILES/g_shared/shared/alberto/projects/spacem-reports/australia-project/initial_reports/metadata_mod_full.csv

Table of Content

1. Ion images plots of DE marker intensities
2. Violin plots of DE marker intensities

Links to ion images for selected markers

	Slide TS33	Slide TS34	Slide TS35	Slide TS36	Slide TS37	Slide TS38
Marker formula
TIC	TIC	TIC	TIC	TIC	TIC	TIC
C16H18O6+Na	2-[2-hydroxy-3-(3-hydroxy...	2-[2-hydroxy-3-(3-hydroxy...	2-[2-hydroxy-3-(3-hydroxy...	2-[2-hydroxy-3-(3-hydroxy...	2-[2-hydroxy-3-(3-hydroxy...	2-[2-hydroxy-3-(3-hydroxy...
C25H47O8P+NH4	PA(2:0/20:1(11Z))	PA(2:0/20:1(11Z))	PA(2:0/20:1(11Z))	PA(2:0/20:1(11Z))	PA(2:0/20:1(11Z))	PA(2:0/20:1(11Z))
C25H50NO8P+H	PC(2:0/15:0)	PC(2:0/15:0)	PC(2:0/15:0)	PC(2:0/15:0)	PC(2:0/15:0)	PC(2:0/15:0)
C30H45NO5+Na	Hydroxybuprenorphine	Hydroxybuprenorphine	Hydroxybuprenorphine	Hydroxybuprenorphine	Hydroxybuprenorphine	Hydroxybuprenorphine
C38H75O7P+NH4	PA(O-13:0/22:1(13Z))	PA(O-13:0/22:1(13Z))	PA(O-13:0/22:1(13Z))	PA(O-13:0/22:1(13Z))	PA(O-13:0/22:1(13Z))	PA(O-13:0/22:1(13Z))
C38H78NO7P+H	PC(0:0/30:0)	PC(0:0/30:0)	PC(0:0/30:0)	PC(0:0/30:0)	PC(0:0/30:0)	PC(0:0/30:0)
C39H78NO6P+NH4	CerP(d18:1(4E)/21:0)	CerP(d18:1(4E)/21:0)	CerP(d18:1(4E)/21:0)	CerP(d18:1(4E)/21:0)	CerP(d18:1(4E)/21:0)	CerP(d18:1(4E)/21:0)
C39H81N2O6P+H	N-hexadecanoylsphinganine...	N-hexadecanoylsphinganine...	N-hexadecanoylsphinganine...	N-hexadecanoylsphinganine...	N-hexadecanoylsphinganine...	N-hexadecanoylsphinganine...
C42H81O10P+NH4	Lysobisphosphatidate (10:...	Lysobisphosphatidate (10:...	Lysobisphosphatidate (10:...	Lysobisphosphatidate (10:...	Lysobisphosphatidate (10:...	Lysobisphosphatidate (10:...
C42H82NO11P+Na	IPC(d18:0/18:1(9Z))	IPC(d18:0/18:1(9Z))	IPC(d18:0/18:1(9Z))	IPC(d18:0/18:1(9Z))	IPC(d18:0/18:1(9Z))	IPC(d18:0/18:1(9Z))
C42H83O7P+NH4	PA(O-13:0/26:1(17Z))	PA(O-13:0/26:1(17Z))	PA(O-13:0/26:1(17Z))	PA(O-13:0/26:1(17Z))	PA(O-13:0/26:1(17Z))	PA(O-13:0/26:1(17Z))
C42H84NO8P+Na	PC(4:0/30:0)	PC(4:0/30:0)	PC(4:0/30:0)	annotation_id C42H84NO8P+Na PC(4:0/30:0) C42H84NO8P+Na PC(14:0/20:0) Name: molecule_name, dtype: object	PC(4:0/30:0)	PC(4:0/30:0)
C42H86NO7P+H	PC(O-13:0/21:0)	PC(O-13:0/21:0)	PC(O-13:0/21:0)	PC(O-13:0/21:0)	PC(O-13:0/21:0)	PC(O-13:0/21:0)
C43H75NO4+Na	Cer(iso-t17:0/26:6(8Z,11Z...	Cer(iso-t17:0/26:6(8Z,11Z...	Cer(iso-t17:0/26:6(8Z,11Z...	Cer(iso-t17:0/26:6(8Z,11Z...	Cer(iso-t17:0/26:6(8Z,11Z...	Cer(iso-t17:0/26:6(8Z,11Z...
C47H83NO4+Na	Cer(iso-t17:0/30:6(12Z,15...	Cer(iso-t17:0/30:6(12Z,15...	Cer(iso-t17:0/30:6(12Z,15...	Cer(iso-t17:0/30:6(12Z,15...	Cer(iso-t17:0/30:6(12Z,15...	Cer(iso-t17:0/30:6(12Z,15...

Ion Images for DE Markers

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Annotation done at FDR 50% against the following databases: HMDB v4, SwissLipids 2018-02-02, KEGG v1

Ion images with TIC normalization: True

TIC

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (TIC)

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Slide TS34 (TIC)

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Slide TS35 (TIC)

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Slide TS36 (TIC)

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Slide TS37 (TIC)

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Slide TS38 (TIC)

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C16H18O6+Na

2-[2-hydroxy-3-(3-hydroxy-4-methoxyphenyl)propyl]benzene-1,3,5-triol, 2-[2-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propyl]benzene-1,3,5-triol, 6-O-Desmethyl-mycophenolic acid, trans-O-Methylgrandmarin

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C16H18O6+Na)

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Slide TS34 (C16H18O6+Na)

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Slide TS35 (C16H18O6+Na)

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Slide TS36 (C16H18O6+Na)

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Slide TS37 (C16H18O6+Na)

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Slide TS38 (C16H18O6+Na)

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C25H47O8P+NH4

PA(2:0/20:1(11Z)), PA(4:0/18:1(6Z)), PA(4:0/18:1(9Z)), PA(4:0/18:1(11E)), PA(4:0/18:1(11Z)), PA(6:0/16:1(6Z)), PA(6:0/16:1(9Z)), PA(8:0/14:1(9Z)), PA(14:1(9Z)/8:0), PA(16:1(6Z)/6:0), PA(16:1(9Z)/6:0), PA(18:1(6Z)/4:0), PA(18:1(9Z)/4:0), PA(18:1(11E)/4:0), PA(18:1(11Z)/4:0), PA(20:1(11Z)/2:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C25H47O8P+NH4)

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Slide TS34 (C25H47O8P+NH4)

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Slide TS35 (C25H47O8P+NH4)

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Slide TS36 (C25H47O8P+NH4)

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Slide TS37 (C25H47O8P+NH4)

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Slide TS38 (C25H47O8P+NH4)

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C25H50NO8P+H

PC(2:0/15:0), PC(3:0/14:0), PC(4:0/13:0), PC(13:0/4:0), PC(14:0/3:0), PC(15:0/2:0), PE(2:0/18:0), PE(3:0/17:0), PE(4:0/16:0), PE(6:0/14:0), PE(8:0/12:0), PE(10:0/10:0), PE(12:0/8:0), PE(14:0/6:0), PE(16:0/4:0), PE(17:0/3:0), PE(18:0/2:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C25H50NO8P+H)

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Slide TS34 (C25H50NO8P+H)

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Slide TS35 (C25H50NO8P+H)

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Slide TS36 (C25H50NO8P+H)

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Slide TS37 (C25H50NO8P+H)

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Slide TS38 (C25H50NO8P+H)

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C30H45NO5+Na

Hydroxybuprenorphine

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C30H45NO5+Na)

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Slide TS34 (C30H45NO5+Na)

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Slide TS35 (C30H45NO5+Na)

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Slide TS36 (C30H45NO5+Na)

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Slide TS37 (C30H45NO5+Na)

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Slide TS38 (C30H45NO5+Na)

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C38H75O7P+NH4

PA(O-13:0/22:1(13Z)), PA(O-15:0/20:1(11Z)), PA(O-17:0/18:1(6Z)), PA(O-17:0/18:1(9Z)), PA(O-17:0/18:1(11E)), PA(O-17:0/18:1(11Z)), PA(O-18:1(9Z)/17:0), PA(O-18:1(11Z)/17:0), PA(O-18:1(13Z)/17:0), PA(O-20:1(11Z)/15:0), PA(O-22:1(13Z)/13:0), PA(P-13:0/22:0), PA(P-14:0/21:0), PA(P-15:0/20:0), PA(P-16:0/19:0), PA(P-17:0/18:0), PA(P-18:0/17:0), PA(P-20:0/15:0), PA(P-22:0/13:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C38H75O7P+NH4)

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Slide TS34 (C38H75O7P+NH4)

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Slide TS35 (C38H75O7P+NH4)

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Slide TS36 (C38H75O7P+NH4)

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Slide TS37 (C38H75O7P+NH4)

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Slide TS38 (C38H75O7P+NH4)

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C38H78NO7P+H

PC(0:0/30:0), PC(30:0/0:0), PC(O-13:0/17:0), PC(O-14:0/16:0), PC(O-15:0/15:0), PC(O-16:0/14:0), PC(O-17:0/13:0), PC(O-18:0/12:0), PC(O-20:0/10:0), PC(O-22:0/8:0), PC(O-24:0/6:0), PC(O-26:0/4:0), PC(O-28:0/2:0), PC(o-14:0/16:0), PE(O-13:0/20:0), PE(O-14:0/19:0), PE(O-15:0/18:0), PE(O-16:0/17:0), PE(O-17:0/16:0), PE(O-18:0/15:0), PE(O-20:0/13:0), PE(O-30:0/3:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C38H78NO7P+H)

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Slide TS34 (C38H78NO7P+H)

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Slide TS35 (C38H78NO7P+H)

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Slide TS36 (C38H78NO7P+H)

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Slide TS37 (C38H78NO7P+H)

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Slide TS38 (C38H78NO7P+H)

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C39H78NO6P+NH4

CerP(d18:1(4E)/21:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C39H78NO6P+NH4)

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Slide TS34 (C39H78NO6P+NH4)

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Slide TS35 (C39H78NO6P+NH4)

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Slide TS36 (C39H78NO6P+NH4)

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Slide TS37 (C39H78NO6P+NH4)

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Slide TS38 (C39H78NO6P+NH4)

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C39H81N2O6P+H

N-hexadecanoylsphinganine-1-phosphocholine, PE-Cer(d14:0/23:0), PE-Cer(d16:0/21:0), PE-Cer(d18:0/19:0), PE-Cer(d20:0/17:0), SM(d14:0/20:0), SM(d16:0/18:0), SM(d18:0/16:0), SM(d20:0/14:0), SM(iso-d17:0/17:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C39H81N2O6P+H)

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Slide TS34 (C39H81N2O6P+H)

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Slide TS35 (C39H81N2O6P+H)

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Slide TS36 (C39H81N2O6P+H)

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Slide TS37 (C39H81N2O6P+H)

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Slide TS38 (C39H81N2O6P+H)

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C42H81O10P+NH4

Lysobisphosphatidate (10:0/0:0/26:1(17Z)/0:0), Lysobisphosphatidate (12:0/0:0/24:1(15Z)/0:0), Lysobisphosphatidate (14:0/0:0/22:1(13Z)/0:0), Lysobisphosphatidate (16:0/0:0/20:1(11Z)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(6Z)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(9Z)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(11E)/0:0), Lysobisphosphatidate (18:0/0:0/18:1(11Z)/0:0), Lysobisphosphatidate (20:0/0:0/16:1(6Z)/0:0), Lysobisphosphatidate (20:0/0:0/16:1(9Z)/0:0), Lysobisphosphatidate (22:0/0:0/14:1(9Z)/0:0), PG(10:0/26:1(17Z)), PG(12:0/24:1(15Z)), PG(14:0/22:1(13Z)), PG(14:1(9Z)/22:0), PG(16:0/20:1(11Z)), PG(16:1(6Z)/20:0), PG(16:1(9Z)/20:0), PG(18:0/18:1(6Z)), PG(18:0/18:1(9Z)), PG(18:0/18:1(11E)), PG(18:0/18:1(11Z)), PG(18:1(6Z)/18:0), PG(18:1(9Z)/18:0), PG(18:1(11E)/18:0), PG(18:1(11Z)/18:0), PG(20:0/16:1(6Z)), PG(20:0/16:1(9Z)), PG(20:1(11Z)/16:0), PG(22:0/14:1(9Z)), PG(22:1(13Z)/14:0), PG(24:1(15Z)/12:0), PG(26:1(17Z)/10:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H81O10P+NH4)

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Slide TS34 (C42H81O10P+NH4)

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Slide TS35 (C42H81O10P+NH4)

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Slide TS36 (C42H81O10P+NH4)

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Slide TS37 (C42H81O10P+NH4)

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Slide TS38 (C42H81O10P+NH4)

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C42H82NO11P+Na

IPC(d18:0/18:1(9Z))

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H82NO11P+Na)

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Slide TS34 (C42H82NO11P+Na)

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Slide TS35 (C42H82NO11P+Na)

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Slide TS36 (C42H82NO11P+Na)

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Slide TS37 (C42H82NO11P+Na)

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Slide TS38 (C42H82NO11P+Na)

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C42H83O7P+NH4

PA(O-13:0/26:1(17Z)), PA(O-15:0/24:1(15Z)), PA(O-17:0/22:1(13Z)), PA(O-18:1(9Z)/21:0), PA(O-18:1(11Z)/21:0), PA(O-18:1(13Z)/21:0), PA(O-20:1(11Z)/19:0), PA(O-22:1(13Z)/17:0), PA(P-13:0/26:0), PA(P-15:0/24:0), PA(P-17:0/22:0), PA(P-18:0/21:0), PA(P-20:0/19:0), PA(P-22:0/17:0), PA(P-24:0/15:0), PA(P-26:0/13:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H83O7P+NH4)

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Slide TS34 (C42H83O7P+NH4)

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Slide TS35 (C42H83O7P+NH4)

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Slide TS36 (C42H83O7P+NH4)

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Slide TS37 (C42H83O7P+NH4)

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Slide TS38 (C42H83O7P+NH4)

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C42H84NO8P+Na

PC(4:0/30:0), PC(6:0/28:0), PC(8:0/26:0), PC(10:0/24:0), PC(12:0/22:0), PC(13:0/21:0), PC(14:0/20:0), PC(15:0/19:0), PC(16:0/18:0), PC(17:0/17:0), PC(18:0/16:0), PC(19:0/15:0), PC(20:0/14:0), PC(21:0/13:0), PC(22:0/12:0), PC(24:0/10:0), PC(26:0/8:0), PC(28:0/6:0), PC(30:0/4:0), PE(13:0/24:0), PE(15:0/22:0), PE(16:0/21:0), PE(17:0/20:0), PE(18:0/19:0), PE(19:0/18:0), PE(20:0/17:0), PE(21:0/16:0), PE(22:0/15:0), PE(24:0/13:0), PE-NMe2(15:0/20:0), PE-NMe2(20:0/15:0), PE-NMe(14:0/22:0), PE-NMe(16:0/20:0), PE-NMe(18:0/18:0), PE-NMe(20:0/16:0), PE-NMe(22:0/14:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H84NO8P+Na)

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Slide TS34 (C42H84NO8P+Na)

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Slide TS35 (C42H84NO8P+Na)

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Slide TS36 (C42H84NO8P+Na)

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Slide TS37 (C42H84NO8P+Na)

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Slide TS38 (C42H84NO8P+Na)

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C42H86NO7P+H

PC(O-13:0/21:0), PC(O-14:0/20:0), PC(O-15:0/19:0), PC(O-16:0/18:0), PC(O-17:0/17:0), PC(O-18:0/16:0), PC(O-20:0/14:0), PC(O-22:0/12:0), PC(O-24:0/10:0), PC(O-26:0/8:0), PC(O-28:0/6:0), PC(O-30:0/4:0), PC(o-16:0/18:0), PE(O-13:0/24:0), PE(O-15:0/22:0), PE(O-16:0/21:0), PE(O-17:0/20:0), PE(O-18:0/19:0), PE(O-20:0/17:0), PE(O-22:0/15:0), PE(O-24:0/13:0)

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C42H86NO7P+H)

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Slide TS34 (C42H86NO7P+H)

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Slide TS35 (C42H86NO7P+H)

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Slide TS36 (C42H86NO7P+H)

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Slide TS37 (C42H86NO7P+H)

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Slide TS38 (C42H86NO7P+H)

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C43H75NO4+Na

Cer(iso-t17:0/26:6(8Z,11Z,14Z,17Z,20Z,23Z))

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C43H75NO4+Na)

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Slide TS34 (C43H75NO4+Na)

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Slide TS35 (C43H75NO4+Na)

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Slide TS36 (C43H75NO4+Na)

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Slide TS37 (C43H75NO4+Na)

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Slide TS38 (C43H75NO4+Na)

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C47H83NO4+Na

Cer(iso-t17:0/30:6(12Z,15Z,18Z,21Z,24Z,27Z))

Joint colormap: for all wells/datasets, the same colormap is used to represent ion intensities.

Slide TS33 (C47H83NO4+Na)

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Slide TS34 (C47H83NO4+Na)

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Slide TS35 (C47H83NO4+Na)

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Slide TS36 (C47H83NO4+Na)

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Slide TS37 (C47H83NO4+Na)

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Slide TS38 (C47H83NO4+Na)

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Violin Plots of Intensities of Differentially Expressed Markers

Violin plots of marker intensities (nonzero only, hotspot-clipped)

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